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When I startup the ide, on the right bottom corner, I keep getting the message "Scanning Project Classpath', and I waited for 48 minutes and nothing changes. This leads to a high disk usage too... org.netbeans.mdr.persistence.StoragePersistentDataException: Bad Magic Number 13 in header at offset 5.823 at org.netbeans.mdr.persistence.btreeimpl.btreestorage.BtreeExtent.readExtent(BtreeExtent.java:149) at org.netbeans.mdr.persistence.btreeimpl.btreestorage.BtreeDataFile.getExtent(BtreeDataFile.java:579) at org.netbeans.mdr.persistence.btreeimpl.btreestorage.BtreeDataFile.checkRecord(BtreeDataFile.java:1009) at org.netbeans.mdr.persistence.btreeimpl.btreestorage.BtreeDataFile.get(BtreeDataFile.java:282) at org.netbeans.mdr.persistence.btreeimpl.btreestorage.BtreeDataFile.get(BtreeDataFile.java:268) at org.netbeans.mdr.persistence.btreeimpl.btreestorage.BtreeDatabase.getRecord(BtreeDatabase.java:979) at org.netbeans.mdr.persistence.btreeimpl.btreestorage.BtreeDatabase.getIfExists(BtreeDatabase.java:731) at org.netbeans.mdr.persistence.btreeimpl.btreestorage.BtreeDatabase.get(BtreeDatabase.java:752) at org.netbeans.mdr.persistence.btreeimpl.btreestorage.BtreeMDRSource.getPage(BtreeMDRSource.java:74) [catch] at org.netbeans.mdr.persistence.btreeimpl.btreeindex.BtreePage.getChild(BtreePage.java:777) at org.netbeans.mdr.persistence.btreeimpl.btreeindex.BtreePage.getLocation(BtreePage.java:607) at org.netbeans.mdr.persistence.btreeimpl.btreeindex.Btree.getLocation(Btree.java:393) at org.netbeans.mdr.persistence.btreeimpl.btreeindex.BtreeListByKey$BtreeListByKeyIterator.<init>(BtreeListByKey.java:146) at org.netbeans.mdr.persistence.btreeimpl.btreeindex.BtreeListByKey.listIterator(BtreeListByKey.java:107) at org.netbeans.mdr.persistence.btreeimpl.btreeindex.BtreeListByKey.isEmpty(BtreeListByKey.java:65) at org.netbeans.mdr.storagemodel.IndexImmutSet.isEmpty(IndexImmutSet.java:95) at org.netbeans.mdr.handlers.IndexSetWrapper.isEmpty(IndexSetWrapper.java:117) at org.netbeans.modules.javacore.JMManager.resolveCPRoot(JMManager.java:1076) at org.netbeans.modules.javacore.JMManager.resolveCodebases(JMManager.java:871) at org.netbeans.modules.javacore.JMManager$2.run(JMManager.java:821) at org.openide.util.RequestProcessor$Task.run(RequestProcessor.java:499) at org.openide.util.RequestProcessor$Processor.run(RequestProcessor.java:932)
Delete var/cache/mdrstorage folder under your userdir (usually in $HOME/.netbeans/5.5) and restart IDE. The part of IDE responsible for this is being completly rewritten in current trunk, so closing as WONTFIX.
Reorganization of java component